Typhoons and associated storm waves in the northwestern Pacific Ocean commonly cause coastal disasters. The possibility remains that an even stronger typhoon than the strongest one observed to date might have occurred before. The development of a method to estimate a maximum intensity of past typhoons over thousands of years is important for paleoclimatology, paleoceanography and disaster prevention. Numerous storm wave boulders exist on reefs in the Ryukyu Islands, Japan, which have been deposited to their present position by the cumulative effects of the past storm waves. These boulders can be used as proxies for the hydrodynamic conditions of the largest waves from past events. Here, we present numerical computations for storm waves and boulder transport with the boulder distribution as a constraint factor to estimate the maximum intensities of storm waves and their causative typhoon events over the past 3500 years. Though the intensities of the maximum estimated waves and associated typhoon events were slightly stronger than those recorded over the past ~70 years in the Ryukyu Islands, our results suggest that no abnormally intense typhoon has struck the Ryukyu Islands in the past 3500 years. The potential impact from tsunamis remains uncertain; however, our results are meteorologically reasonable.